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The automotive industry is transitioning from traditional ECU-based systems to software-defined vehicles. A central role of this revolution is played by containers, lightweight virtualization technologies that enable the flexible…
The emergence of Software-Defined Vehicles (SDVs) signifies a shift from a distributed network of electronic control units (ECUs) to a centralized computing architecture within the vehicle's electrical and electronic systems. This…
The drug discovery process involves several tasks to be performed in vivo, in vitro and in silico. Molecular docking is a task typically performed in silico. It aims at finding the three-dimensional pose of a given molecule when it…
This project investigates the benefits of containerization technology in modern software development and deployment. The study emphasizes the advantages of using Kubernetes and Docker in the development process, including the easy packaging…
COVID-19 has shown the importance of having a fast response against pandemics. Finding a novel drug is a very long and complex procedure, and it is possible to accelerate the preliminary phases by using computer simulations. In particular,…
Heterogeneity has been an indispensable aspect of distributed computing throughout the history of these systems. In particular, with the increasing prevalence of accelerator technologies (e.g., GPUs and TPUs) and the emergence of…
In this work, we propose a deep learning approach to improve docking-based virtual screening. The introduced deep neural network, DeepVS, uses the output of a docking program and learns how to extract relevant features from basic data such…
Drug discovery through virtual screening (VS) has become a popular strategy for identifying hits against protein targets. Alongside VS, molecular design further expands accessible chemical space. Together, these approaches have the…
Stacking (or stacked generalization) is an ensemble learning method with one main distinctiveness from the rest: even though several base models are trained on the original data set, their predictions are further used as input data for one…
Heterogeneous systems are present from powerful supercomputers, to mobile devices, including desktop computers, thanks to their excellent performance and energy consumption. The ubiquity of these architectures in both desktop systems and…
Container technique is gaining increasing attention in recent years and has become an alternative to traditional virtual machines. Some of the primary motivations for the enterprise to adopt the container technology include its convenience…
Existing benchmarking methods are time consuming processes as they typically benchmark the entire Virtual Machine (VM) in order to generate accurate performance data, making them less suitable for real-time analytics. The research in this…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
Many existing scientific workflows require High Performance Computing environments to produce results in a timely manner. These workflows have several software library components and use different environments, making the deployment and…
Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation…
High-performance computing (HPC) is reshaping computational drug discovery by enabling large-scale, time-efficient molecular simulations. In this work, we explore HPC-driven pipelines for Alzheimer's disease drug discovery, focusing on…
High-throughput structure-based screening of drug-like molecules has become a common tool in biomedical research. Recently, acceleration with graphics processing units (GPUs) has provided a large performance boost for molecular docking…
Machine learning shows great potential in virtual screening for drug discovery. Current efforts on accelerating docking-based virtual screening do not consider using existing data of other previously developed targets. To make use of the…
Molecular docking, a technique for predicting ligand binding poses, is crucial in structure-based drug design for understanding protein-ligand interactions. Recent advancements in docking methods, particularly those leveraging geometric…
With the availability of a wide range of cloud Virtual Machines (VMs) it is difficult to determine which VMs can maximise the performance of an application. Benchmarking is commonly used to this end for capturing the performance of VMs.…